millironx/taxprofiler
1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-11-22 07:09:56 +00:00
Code Issues Releases Packages Activity

Fix input channels to kraken2

Browse source
This commit is contained in:
James Fellows Yates 2022-03-26 06:45:16 +01:00
parent 000f129dab
commit 120382f51d
1 changed files with 6 additions and 6 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

12
workflows/taxprofiler.nf
View file

@ -37,11 +37,11 @@ ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multi
// //
// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
// //
include { INPUT_CHECK } from '../subworkflows/local/input_check' include { INPUT_CHECK } from '../subworkflows/local/input_check'
include { DB_CHECK } from '../subworkflows/local/db_check' include { DB_CHECK } from '../subworkflows/local/db_check'
include { SHORTREAD_PREPROCESSING } from '../subworkflows/local/shortread_preprocessing' include { SHORTREAD_PREPROCESSING } from '../subworkflows/local/shortread_preprocessing'
include { LONGREAD_PREPROCESSING } from '../subworkflows/local/longread_preprocessing' include { LONGREAD_PREPROCESSING } from '../subworkflows/local/longread_preprocessing'
/* /*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@ -171,7 +171,7 @@ workflow TAXPROFILER {
[ temp_meta, it[1], db ] [ temp_meta, it[1], db ]
} }
.groupTuple(by: [0,2]) .groupTuple(by: [0,2])
.dump(tag: "input for malt") .dump(tag: "input_for_malt")
.multiMap { .multiMap {
it -> it ->
reads: [ it[0], it[1].flatten() ] reads: [ it[0], it[1].flatten() ]
@ -180,10 +180,10 @@ workflow TAXPROFILER {
// We can run Kraken2 one-by-one sample-wise // We can run Kraken2 one-by-one sample-wise
ch_input_for_kraken2 = ch_input_for_profiling.kraken2 ch_input_for_kraken2 = ch_input_for_profiling.kraken2
.dump(tag: "input for kraken") .dump(tag: "input_for_kraken")
.multiMap { .multiMap {
it -> it ->
reads: [ it[0] + it[2], it[1] ] reads: [ it[0] + it[2], it[1].flatten() ]
db: it[3] db: it[3]
} }